data_XTR
# 
_chem_comp.id                                    XTR 
_chem_comp.name                                  "[(1R,4S,6S)-6-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclohex-2-en-1-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C12 H17 N2 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2009-01-05 
_chem_comp.pdbx_modified_date                    2011-06-04 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         HDP 
_chem_comp.formula_weight                        332.246 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     XTR 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        3FL6 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
XTR OP3    O3P    O 0 1 N Y N 20.825 39.982 30.214 -5.512 0.209  -1.373 OP3    XTR 1  
XTR "C4'"  "C4'"  C 0 1 N N R 23.416 38.455 28.045 -1.052 -1.397 0.225  "C4'"  XTR 2  
XTR "C7'"  "C7'"  C 0 1 N N N 22.201 36.500 29.020 0.661  -1.453 -1.555 "C7'"  XTR 3  
XTR "C6'"  "C6'"  C 0 1 N N N 22.898 37.634 29.192 -0.570 -1.284 -1.192 "C6'"  XTR 4  
XTR "C1'"  "C1'"  C 0 1 N N S 21.830 35.947 27.668 1.780  -1.774 -0.609 "C1'"  XTR 5  
XTR O4     O4     O 0 1 N N N 16.787 34.005 28.587 4.770  2.638  0.261  O4     XTR 6  
XTR C4     C4     C 0 1 N N N 17.886 34.502 28.379 4.088  1.647  0.067  C4     XTR 7  
XTR C5     C5     C 0 1 N N N 18.127 35.908 28.154 2.681  1.711  0.203  C5     XTR 8  
XTR C5M    C5M    C 0 1 N N N 16.974 36.860 28.176 2.008  3.003  0.588  C5M    XTR 9  
XTR C6     C6     C 0 1 N N N 19.390 36.279 27.942 1.948  0.598  -0.019 C6     XTR 10 
XTR N3     N3     N 0 1 N N N 19.008 33.704 28.335 4.667  0.481  -0.284 N3     XTR 11 
XTR C2     C2     C 0 1 N N N 20.313 34.076 28.119 3.913  -0.613 -0.499 C2     XTR 12 
XTR O2     O2     O 0 1 N N N 21.215 33.251 28.111 4.449  -1.658 -0.815 O2     XTR 13 
XTR N1     N1     N 0 1 N N N 20.478 35.431 27.915 2.575  -0.567 -0.369 N1     XTR 14 
XTR "C2'"  "C2'"  C 0 1 N N N 21.909 36.975 26.530 1.217  -2.283 0.720  "C2'"  XTR 15 
XTR "C3'"  "C3'"  C 0 1 N N S 23.177 37.693 26.761 0.131  -1.309 1.192  "C3'"  XTR 16 
XTR P      P      P 0 1 N N N 21.673 41.251 29.700 -4.439 0.612  -0.242 P      XTR 17 
XTR OP1    O1P    O 0 1 N N N 22.204 42.048 30.839 -3.955 1.988  -0.489 OP1    XTR 18 
XTR OP2    O2P    O 0 1 N N N 20.754 41.858 28.709 -5.136 0.540  1.208  OP2    XTR 19 
XTR "O5'"  "O5'"  O 0 1 N N N 22.935 40.620 28.978 -3.197 -0.411 -0.291 "O5'"  XTR 20 
XTR "C5'"  "C5'"  C 0 1 N N N 22.655 39.737 27.896 -2.030 -0.258 0.520  "C5'"  XTR 21 
XTR "O3'"  "O3'"  O 0 1 N N N 24.193 36.755 26.384 -0.297 -1.667 2.507  "O3'"  XTR 22 
XTR HOP3   HO3P   H 0 0 N N N 20.658 39.396 29.485 -6.289 0.784  -1.401 HO3P   XTR 23 
XTR "H4'"  "H4'"  H 0 1 N N N 24.479 38.660 28.240 -1.558 -2.353 0.359  "H4'"  XTR 24 
XTR "H7'"  "H7'"  H 0 1 N N N 21.889 35.954 29.898 0.897  -1.356 -2.605 "H7'"  XTR 25 
XTR "H6'"  "H6'"  H 0 1 N N N 23.095 37.971 30.199 -1.296 -1.049 -1.957 "H6'"  XTR 26 
XTR "H1'"  "H1'"  H 0 1 N N N 22.529 35.179 27.304 2.416  -2.543 -1.048 "H1'"  XTR 27 
XTR H5M    H5M    H 0 1 N N N 16.711 37.094 29.218 2.762  3.780  0.721  H5M    XTR 28 
XTR H5MA   H5MA   H 0 0 N N N 17.253 37.786 27.652 1.315  3.301  -0.199 H5MA   XTR 29 
XTR H5MB   H5MB   H 0 0 N N N 16.110 36.400 27.674 1.461  2.865  1.520  H5MB   XTR 30 
XTR H6     H6     H 0 1 N N N 19.577 37.330 27.778 0.873  0.628  0.080  H6     XTR 31 
XTR HN3    HN3    H 0 1 N N N 18.853 32.727 28.479 5.631  0.430  -0.382 HN3    XTR 32 
XTR "H2'"  "H2'"  H 0 1 N N N 21.908 36.479 25.548 0.785  -3.274 0.579  "H2'"  XTR 33 
XTR "H2'A" "H2'A" H 0 0 N N N 21.044 37.654 26.525 2.015  -2.331 1.462  "H2'A" XTR 34 
XTR "H3'"  "H3'"  H 0 1 N N N 23.166 38.605 26.146 0.526  -0.293 1.196  "H3'"  XTR 35 
XTR "H5'"  "H5'"  H 0 1 N N N 22.949 40.221 26.953 -2.313 -0.285 1.572  "H5'"  XTR 36 
XTR "H5'A" "H5'A" H 0 0 N N N 21.579 39.511 27.894 -1.555 0.697  0.296  "H5'A" XTR 37 
XTR "HO3'" "HO3'" H 0 0 N Y N 24.106 36.547 25.461 0.408  -1.648 3.169  "HO3'" XTR 38 
XTR HOP2   HO2P   H 0 0 N N N 19.901 41.988 29.106 -5.478 -0.335 1.438  HO2P   XTR 39 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
XTR OP3   HOP3   SING N N 1  
XTR "C4'" "C6'"  SING N N 2  
XTR "C4'" "H4'"  SING N N 3  
XTR "C7'" "C6'"  DOUB N N 4  
XTR "C7'" "H7'"  SING N N 5  
XTR "C6'" "H6'"  SING N N 6  
XTR "C1'" "C7'"  SING N N 7  
XTR "C1'" N1     SING N N 8  
XTR "C1'" "H1'"  SING N N 9  
XTR C4    O4     DOUB N N 10 
XTR C5    C4     SING N N 11 
XTR C5    C5M    SING N N 12 
XTR C5M   H5M    SING N N 13 
XTR C5M   H5MA   SING N N 14 
XTR C5M   H5MB   SING N N 15 
XTR C6    C5     DOUB N N 16 
XTR C6    H6     SING N N 17 
XTR N3    C4     SING N N 18 
XTR N3    HN3    SING N N 19 
XTR C2    N3     SING N N 20 
XTR O2    C2     DOUB N N 21 
XTR N1    C6     SING N N 22 
XTR N1    C2     SING N N 23 
XTR "C2'" "C1'"  SING N N 24 
XTR "C2'" "C3'"  SING N N 25 
XTR "C2'" "H2'"  SING N N 26 
XTR "C2'" "H2'A" SING N N 27 
XTR "C3'" "C4'"  SING N N 28 
XTR "C3'" "H3'"  SING N N 29 
XTR P     OP3    SING N N 30 
XTR P     OP1    DOUB N N 31 
XTR OP2   P      SING N N 32 
XTR "O5'" P      SING N N 33 
XTR "C5'" "C4'"  SING N N 34 
XTR "C5'" "O5'"  SING N N 35 
XTR "C5'" "H5'"  SING N N 36 
XTR "C5'" "H5'A" SING N N 37 
XTR "O3'" "C3'"  SING N N 38 
XTR "O3'" "HO3'" SING N N 39 
XTR OP2   HOP2   SING N N 40 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
XTR SMILES           ACDLabs              10.04 "O=P(O)(O)OCC2C=CC(N1C=C(C(=O)NC1=O)C)CC2O"                                                                                                               
XTR SMILES_CANONICAL CACTVS               3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)C=C2)C(=O)NC1=O"                                                                                              
XTR SMILES           CACTVS               3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)C=C2)C(=O)NC1=O"                                                                                                  
XTR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](C=C2)COP(=O)(O)O)O"                                                                                                
XTR SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(C=C2)COP(=O)(O)O)O"                                                                                                             
XTR InChI            InChI                1.03  "InChI=1S/C12H17N2O7P/c1-7-5-14(12(17)13-11(7)16)9-3-2-8(10(15)4-9)6-21-22(18,19)20/h2-3,5,8-10,15H,4,6H2,1H3,(H,13,16,17)(H2,18,19,20)/t8-,9-,10+/m1/s1" 
XTR InChIKey         InChI                1.03  PIQIDTLVJACCCC-BBBLOLIVSA-N                                                                                                                               
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
XTR "SYSTEMATIC NAME" ACDLabs              10.04 "[(1R,4S,6S)-6-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclohex-2-en-1-yl]methyl dihydrogen phosphate" 
XTR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(1R,4S,6S)-6-hydroxy-4-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-1-cyclohex-2-enyl]methyl dihydrogen phosphate"                
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
XTR "Create component"  2009-01-05 RCSB 
XTR "Modify descriptor" 2011-06-04 RCSB 
# 
